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ankane / jetpack

A friendly package manager for R
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Issues with BioConductor packages #18

Closed rprops closed 4 years ago

rprops commented 4 years ago

Dear,

I've been trying to get jetpack to work for my repo. But I'm running into some issues with Bioconductor packages as dependencies.

I ran:

jetpack::init()
jetpack::add("Phenoflow", remote="CMET-UGent/Phenoflow_package")

But got the following warning:

Installing BiocGenerics (0.32.0) ... 
FAILED
Error: Failed to retrieve package sources for BiocGenerics 0.32.0 from CRAN (internet connectivity issue?)

I've tried the suggested solution on packrat, but to no avail. (https://github.com/rstudio/packrat/issues/507)

jetpack::init()
options(repos=structure(BiocManager::repositories()))
jetpack::add("Phenoflow", remote="CMET-UGent/Phenoflow_package")

Any suggestions?

Thank you!

Ruben

ankane commented 4 years ago

Hey @rprops, can you give the bioconductor2 branch a shot?

remotes::install_github("ankane/jetpack@bioconductor2")

Then restart your R session and do:

jetpack::add(c("BiocManager", "BiocGenerics"))
ankane commented 4 years ago

On 2nd thought, not really happy with that approach. Instead, try updating the Repos: line in your packrat.lock manually to something like this:

Repos: CRAN=https://cloud.r-project.org/,
    BioCsoft=https://bioconductor.org/packages/3.10/bioc,
    BioCann=https://bioconductor.org/packages/3.10/data/annotation,
    BioCexp=https://bioconductor.org/packages/3.10/data/experiment,
    BioCworkflows=https://bioconductor.org/packages/3.10/workflows

(no need to use the branch above)

rprops commented 4 years ago

Already tried solution 1 and seems to have worked - I'll check out solution 2 later. Thanks for the quick fix @ankane !

ankane commented 4 years ago

Updated the instructions here: https://github.com/ankane/jetpack#bioconductor